[English] 日本語
Yorodumi
- PDB-7l4s: Crystal structure of the OxyR regulatory domain of Shewanella one... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l4s
TitleCrystal structure of the OxyR regulatory domain of Shewanella oneidensis MR-1, reduced form
ComponentsTranscriptional regulator of oxidative stress OxyR
KeywordsDNA BINDING PROTEIN / OxyR
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding => GO:0000987 / protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator of oxidative stress OxyR
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTao, Y.J. / Gao, H.
Funding support United States, China, 4items
OrganizationGrant numberCountry
Robert A. Welch FoundationC-1565 United States
Ministry of Science and Technology (MoST, China)2018YFA0901300 China
National Natural Science Foundation of China (NSFC)41976087 China
National Natural Science Foundation of China (NSFC)31930003 China
CitationJournal: Mbio / Year: 2022
Title: Functional Irreplaceability of Escherichia coli and Shewanella oneidensis OxyRs Is Critically Determined by Intrinsic Differences in Oligomerization.
Authors: Sun, W. / Fan, Y. / Wan, F. / Tao, Y.J. / Gao, H.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator of oxidative stress OxyR
B: Transcriptional regulator of oxidative stress OxyR
C: Transcriptional regulator of oxidative stress OxyR
D: Transcriptional regulator of oxidative stress OxyR
E: Transcriptional regulator of oxidative stress OxyR
F: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)202,8726
Polymers202,8726
Non-polymers00
Water6,071337
1
A: Transcriptional regulator of oxidative stress OxyR
C: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)67,6242
Polymers67,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-11 kcal/mol
Surface area17930 Å2
MethodPISA
2
B: Transcriptional regulator of oxidative stress OxyR
D: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)67,6242
Polymers67,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-10 kcal/mol
Surface area17440 Å2
MethodPISA
3
E: Transcriptional regulator of oxidative stress OxyR

F: Transcriptional regulator of oxidative stress OxyR


Theoretical massNumber of molelcules
Total (without water)67,6242
Polymers67,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_864-y+3,x-y+1,z-1/31
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.998, 83.998, 185.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

-
Components

#1: Protein
Transcriptional regulator of oxidative stress OxyR


Mass: 33811.957 Da / Num. of mol.: 6 / Fragment: Regulatory domain / Mutation: C203S
Source method: isolated from a genetically manipulated source
Details: OxyR RD domain with C203S mutation and 6xHis tag at the N-terminus
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: oxyR, SO_1328 / Plasmid: pET-28a(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q8EHA1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.83 % / Description: Rod-shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Drops were made by combining 1 ul of SoOxyR C203S RD with 1 ul of mother liquor containing 4.0 M ammonium acetate and 0.1 M Bis-Tris propane pH 7.0. Rod-shaped crystals appeared within 3 to 4 days.

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 57163 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.509 / Num. unique obs: 2815 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i69

1i69


Resolution: 2.4→42 Å / Cross valid method: FREE R-VALUE / σ(F): 182.18 / Phase error: 25.6731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 2830 4.96 %
Rwork0.1744 54280 -
obs0.1931 57110 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 0 337 9621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00549446
X-RAY DIFFRACTIONf_angle_d0.890112839
X-RAY DIFFRACTIONf_chiral_restr0.05291585
X-RAY DIFFRACTIONf_plane_restr0.00731612
X-RAY DIFFRACTIONf_dihedral_angle_d5.69351260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.31361360.25432691X-RAY DIFFRACTION94.92
2.44-2.490.30971420.24322708X-RAY DIFFRACTION95.02
2.49-2.530.31921520.23492713X-RAY DIFFRACTION94.69
2.53-2.580.29191720.22432675X-RAY DIFFRACTION93.96
2.58-2.640.27891520.2192710X-RAY DIFFRACTION94.69
2.64-2.70.23441170.2292781X-RAY DIFFRACTION95.9
2.7-2.770.3105900.20382724X-RAY DIFFRACTION96.8
2.77-2.840.25841340.2072713X-RAY DIFFRACTION95.29
2.84-2.930.28591500.20762705X-RAY DIFFRACTION94.75
2.93-3.020.28861360.20222728X-RAY DIFFRACTION95.25
3.02-3.130.23491480.19632744X-RAY DIFFRACTION94.88
3.13-3.260.27461320.18592735X-RAY DIFFRACTION95.4
3.26-3.40.24941650.19272658X-RAY DIFFRACTION94.16
3.4-3.580.19271100.18822751X-RAY DIFFRACTION96.09
3.58-3.810.23591680.17552704X-RAY DIFFRACTION94.15
3.81-4.10.19551600.17072671X-RAY DIFFRACTION94.18
4.1-4.510.19541650.16042701X-RAY DIFFRACTION94.18
4.51-5.160.1861400.14862725X-RAY DIFFRACTION95.11
5.17-6.50.24231610.18152704X-RAY DIFFRACTION94.38
6.51-420.2237980.20832741X-RAY DIFFRACTION95.84

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more